A predictive controller controls a system under uncertainty subject to constraints on state and control variables of the system. At each control step, the predictive controller solves an inequality constrained nonlinear dynamic optimization problem including probabilistic chance constraints representing the uncertainty to produce a control command, and controls an operation of the system using the control command. The predictive controller solves the dynamic optimization problem based on a two-level optimization that alternates, until a termination condition is met, propagation of covariance matrices of the probabilistic chance constraints within the prediction horizon for fixed values of the state and control variables with optimization of the state and control variables within the prediction horizon for fixed values of the covariance matrices.